Not sure this will help since you are using the vault server to manage the content center... But without Inventor running go to
For XP: C:\Document and Settings\<user name>\Local Settings\Application Data\Autodesk and rename your Inventor <version> folder to Inventor <version>_OLD...
For Win 7: C:\Users\lancasterm\AppData\Local\Autodesk and rename your Inventor <version> folder to Inventor <version>_OLD...
Restart Inventor and let it recreate the content center caching files/folder.
Just wondering if your local CC caching files are not being updating (I have seen this before and deleting the CC caching folders fixed the problem).... So Inventor continues to think the information in your model is up to date even though its not.
Side note: If you created favorites in your CC this information is also stored under that folder structure... If you did, you can rename the sub-folder Content Center to Content Center OLD
Ok I was going back over the replies and have a couple more questiongs/thoughts... When you do a refresh of standard components are you getting any message? If no, do you have a user created LOD active? Also are the local content center part set to read only on your hard drive? Sometimes that happens when data has been migrated and you have to remove the read only attribute from the file itself. Do you have any (mapped) custom IPROPERTIES in the family table with blank cells. If you do then you need a formula (typed) as &" "& for the given blank to create a space for that IPROPERTIES.